Mercurial > repos > iuc > multiqc

diff multiqc.xml @ 26:d2aaac19f42f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
author iuc
date Tue, 11 Feb 2025 10:13:08 +0000
parents f7e2f1eb3a16
children 7591bce96601
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line diff
--- a/multiqc.xml	Sat Jan 25 17:24:12 2025 +0000
+++ b/multiqc.xml	Tue Feb 11 10:13:08 2025 +0000
@@ -23,6 +23,7 @@
         <import>star_plugin.xml</import>
         <import>trimmomatic_plugin.xml</import>
         <import>vcftools_plugin.xml</import>
+        <import>sambamba_plugin.xml</import>
     </macros>
     <expand macro="bio_tools"/>
     <expand macro="requirements"/>
@@ -143,6 +144,8 @@
         @TRIMMOMATIC_COMMAND@
     #elif str($repeat.software_cond.software) == "vcftools"
         @VCFTOOLS_COMMAND@
+    #elif str($repeat.software_cond.software) == "sambamba"
+        @SAMBAMBA_COMMAND@
     #else if str($repeat.software_cond.software) == "custom_content":
         #set $configfile = "T"
         #for $j, $file in enumerate( $repeat.software_cond.input )
@@ -236,6 +239,7 @@
                     <!--<option value="salmon">Salmon</option>-->
                     <option value="samblaster">Samblaster</option>
                     <option value="samtools">Samtools</option>
+                    <option value="sambamba">Sambamba</option>
                     <!--<option value="sargasso">Sargasso</option>-->
                     <!--<option value="seqyclean">SeqyClean</option>-->
                     <!--<option value="sexdeterrmine">SexDetErrmine</option>-->
@@ -349,6 +353,9 @@
                 <when value="vcftools">
                     <expand macro="vcftools_form"/>
                 </when>
+                <when value="sambamba">
+                    <expand macro="sambamba_form"/>
+                </when>
                 <when value="custom_content">
                     <param argument="plot_type" label="The plot type to visualise the data with" type="select">
                         <option value="linegraph">linegraph</option>
@@ -425,6 +432,7 @@
         <expand macro="gatk_test"/>
         <expand macro="bamtools_test"/>
         <expand macro="pycoqc_test"/>
+        <expand macro="sambamba_test"/>
 
         <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->